Pacific Symposium on Biocomputing papers

The AMP: Assembly Matching Pursuit paper featured Saturday came from the Pacific Symposium on Biocomputing conference for which the complete online proceedings can be found here (the twitter account for the conference is @PacSymBiocomp and the hashtag used by conference attendees is #psb13). Here is the list of papers presented there:

Computational drug repositioning

• Session Introduction Zhiyong Lu, Pankaj Agarwal, and Atul Butte; Pacific Symposium on Biocomputing 18:1-4(2013)
• Evaluation of Analytical Methods for Connectivity Map DataJie Cheng, Qing Xie, Vinod Kumar, Mark Hurle, Johannes M. Freudenberg, Lun Yang, Pankaj Agarwal ; Pacific Symposium on Biocomputing 18:5-16(2013)
• Predictive Systems Biology Approach to Broad-Spectrum, Host-Directed Drug Target Discovery in Infectious DiseasesRamon M. Felciano, Sina Bavari, Daniel R. Richards, Jean-Noel Billaud, Travis Warren, Rekha Panchal, Andreas Kraemer; Pacific Symposium on Biocomputing 18:17-28(2013)
• A Novel Multi-Modal Drug Repurposing Approach for Identification of Potent ACK1 InhibitorsSharangdhar S. Phatak, Shuxing Zhang; Pacific Symposium on Biocomputing 18:29-40(2013)
• Protein-chemical Interaction Prediction via Kernelized Sparse Learning SVMYi Shi, Xinhua Zhang, Xiaoping Liao, Guohui Lin, Dale Schuurmans; Pacific Symposium on Biocomputing 18:41-52(2013)
• Drug Target Predictions Based on Heterogeneous Graph InferenceWenhui Wang, Sen Yang, Jing Li; Pacific Symposium on Biocomputing 18:53-64(2013)

Epigenomics

• Session IntroductionAlexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng; Pacific Symposium on Biocomputing 18:65-68(2013)
• A Powerful Statistical Method for Identifying Differentially Methylated Markers in Complex DiseasesSurin Ahn, Tao Wang; Pacific Symposium on Biocomputing 18:69-79(2013)
• Using DNase Digestion Data to Accurately Identify Transcription Factor Binding SitesKaixuan Luo, Alexander J. Hartemink; Pacific Symposium on Biocomputing 18:80-91(2013)
• Epigenomic Model of Cardiac Enhancers with Application to Genome Wide Association StudiesAvinash Das Sahu, Radhouane Aniba, Yen-Pei Christy Chang, Sridhar Hannenhalli; Pacific Symposium on Biocomputing 18:92-102(2013)

Identification of Aberrant Pathway and Network Activity from High-Throughput Data

• Session IntroductionRachel Karchin, Michael F. Ochs, Joshua M. Stuart, Trey Ideker, Joel S. Bader; Pacific Symposium on Biocomputing 18:103-110(2013)
• From Uncertain Protein Interaction Networks to Signaling Pathways Through Intensive Color CodingHaitham Gabr, Alin Dobra, Tamer Kahveci; Pacific Symposium on Biocomputing 18:111-122(2013)
• Identifying Master Regulators of Cancer and Their Downstream Targets by Integrating Genomic and Epigenomic FeaturesOlivier Gevaert, Sylvia Plevritis; Pacific Symposium on Biocomputing 18:123-134(2013)
• Module Cover - A New Approach to Genotype-Phenotype StudiesYoo-Ah Kim, Raheleh Salari, Stefan Wuchty, Teresa M. Przytycka; Pacific Symposium on Biocomputing 18:135-146(2013)
• Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX ToolkitSarah A. Pendergrass, Shefali S. Verma, Emily R. Holzinger, Carrie B. Moore, John Wallace, Scott M. Dudek, Wayne Huggins, Terrie Kitchner, Carol Waudby, Richard Berg, Catherine A. McCarty, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 18:147-158(2013)
• Interpreting Personal Transcriptomes: Personalized Mechanism-Scale Profiling of RNA-seq DataAlan Perez-Rathke, Haiquan Li, Yves A. Lussier; Pacific Symposium on Biocomputing 18:159-170(2013)

Personalized medicine: from genotypes and molecular phenotypes towards therapy

• Session introductionOliver Stegle, Steven E. Brenner, Quaid Morris, Jennifer Listgarten; Pacific Symposium on Biocomputing 18:171-174(2013)
• AMP: Assembly Matching PursuitSurojit Biswas, Vladimir Jojic; Pacific Symposium on Biocomputing 18:175-187(2013)
• Characterization of the Metabochip in Diverse Populations from the International HapMap Project in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) ProjectDana C. Crawford, Robert Goodloe, Kristin Brown-Gentry, Sarah Wilson, Jamie Roberson, Niloufar B. Gillani, Marylyn D. Ritchie, Holli H. Dilks, William S. Bush ; Pacific Symposium on Biocomputing 18:188-199(2013)
• Insights into Diseases of Human Telomerase from Dynamical ModelingSamuel Coulbourn Flores, Georgeta Zemora, Christina Waldsich; Pacific Symposium on Biocomputing 18:200-211(2013)
• Spectral Clustering Strategies for Heterogeneous Disease DataGrace T. Huang, Kathryn I. Cunningham, Panayiotis V. Benos, Chakra S. Chennubhotla; Pacific Symposium on Biocomputing 18:212-223(2013)
• Systematic Identification of Risk Factors for Alzheimer's Disease Through Shared Genetic Architecture and Electronic Medical RecordsLi Li, David Ruau, Rong Chen, Susan Weber, Atul J. Butte; Pacific Symposium on Biocomputing 18:224-235(2013)
• A Correlated Meta-Analysis Strategy for Data Mining “Omic” ScansMichael A. Province, Ingrid B. Borecki; Pacific Symposium on Biocomputing 18:236-246(2013)

Phylogenomics and Population Genomics: Models, Algorithms, and Analytical Tools

• Session introductionLuay Nakhleh, Noah Rosenberg, Tandy Warnow; Pacific Symposium on Biocomputing 18:247-249(2013)
• Inferring Optimal Species Trees Under Gene Duplication and LossM.S. Bayzid, Siavash Mirarab, Tandy Warnow; Pacific Symposium on Biocomputing 18:250-261(2013)
• Evaluating Variations on the STAR Algorithm for Relative Efficiency and Sample Sizes Needed to Reconstruct Species TreesJames H. Degnan; Pacific Symposium on Biocomputing 18:262-272(2013)
• The Behavior of Admixed Populations in Neighbor-Joining Inference of Population TreesNaama M. Kopelman, Lewi Stone, Olivier Gascuel, Noah A. Rosenberg; Pacific Symposium on Biocomputing 18:273-284(2013)
• Maximum Likelihood Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Tree of 68 EukaryotesYu Lin, Fei Hu, Jijun Tang, Bernard M.E. Moret; Pacific Symposium on Biocomputing 18:285-296(2013)
• An Analytical Comparison of Multilocus Methods Under the Multispecies Coalescent: The Three-Taxon CaseSebastien Roch; Pacific Symposium on Biocomputing 18:297-306(2013)

Post-NGS: Interpretation and Analysis of Next Generation Sequencing Data for Basic and Translational Science

• Session introductionGurkan Bebek, Mehmet Koyuturk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance; Pacific Symposium on Biocomputing 18:307-309(2013)
• LSHPlace: Fast Phylogenetic Placement Using Locality-Sensitive HashingDaniel G. Brown, Jakub Truszkowski; Pacific Symposium on Biocomputing 18:310-319(2013)
• ChIPModule: Systematic Discovery of Transcription Factors and Their Cofactors from ChIP-seq DataJun Ding, Xiaohui Cai, Ying Wang, Haiyan Hu, Xiaoman Li; Pacific Symposium on Biocomputing 18:320-331(2013)
• Using BioBin to Explore Rare Variant Population StratificationCarrie B. Moore, John R. Wallace, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 18:332-343(2013)
• Detecting Highly Differentiated Copy-Number Variants from Pooled Population SequencingDaniel R. Schrider, David J. Begun, Matthew W. Hahn; Pacific Symposium on Biocomputing 18:344-355(2013)
• MetaSeq: Privacy Preserving Meta-Analysis of Sequencing-Based Association StudiesAngad Pal Singh, Samreen Zafer, Itsik Pe'er; Pacific Symposium on Biocomputing 18:356-367(2013)

Text and Data Mining for Biomedical Discovery

• Session introductionGraciela H. Gonzalez, Kevin Bretonnel Cohen, Casey Greene, Udo Hahn, Maricel G. Kann, Robert Leaman, Nigam Shah, Jieping Ye; Pacific Symposium on Biocomputing 18:368-372(2013)
• Enabling High-Throughput Genotype-Phenotype Associations in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) Project as Part of the Population Architecture Using Genomics and Epidemiology (PAGE) StudyWilliam S. Bush, Jonathan Boston, Sarah A. Pendergrass, Logan Dumitrescu, Robert Goodloe, Kristin Brown-Gentry, Sarah Wilson, Bob McClellan Jr., Eric Torstenson, Melissa A. Basford, Kylee L. Spencer, Marylyn D. Ritchie, Dana C. Crawford; Pacific Symposium on Biocomputing 18:373-384(2013)
• ATHENA: A Tool for Meta-Dimensional Analysis Applied to Genotypes and Gene Expression Data to Predict HDL Cholesterol LevelsEmily R Holzinger, Scott M. Dudek, Alex T. Frase, Ronald M. Krauss, Marisa W. Medina, Marylyn D. Ritchie; Pacific Symposium on Biocomputing 18:385-396(2013)
• Statistical Epistasis Networks Reduce the Computational Complexity of Searching Three-Locus Genetic ModelsTing Hu, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore; Pacific Symposium on Biocomputing 18:397-408(2013)
• Evaluation of Linear Classifiers on Articles Containing Pharmacokinetic Evidence of Drug-Drug InteractionsArtemy Kolchinsky, Analia Lourenco, Lang Li, Luis M. Rocha; Pacific Symposium on Biocomputing 18:409-420(2013)
• Incorporating Expert Terminology and Disease Risk Factors into Consumer Health VocabulariesMichael Seedorff, Kevin J. Peterson, Laurie A. Nelsen, Cristian Cocos, Jennifer B. McCormick, Christopher G. Chute, Jyotishman Pathak; Pacific Symposium on Biocomputing 18:421-432(2013)
• Detection of Protein Catalytic Sites in the Biomedical LiteratureKarin Verspoor, Andrew MacKinlay, Judith D. Cohn, Michael E. Wall; Pacific Symposium on Biocomputing 18:433-444(2013)
• WorkshopsModeling cell heterogeneity: from single-cell variations to mixed cells populationsEric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, and Damian Wojtowicz; Pacific Symposium on Biocomputing 18:445-450(2013)
• Computational Biology in the Cloud: Methods and New Insights from Computing at ScalePeter M. Kasson; Pacific Symposium on Biocomputing 18:451-453(2013)
• Computational Challenges of Mass PhenotypingLawrence Hunter; Pacific Symposium on Biocomputing 18:454-455(2013)
• The Future of Genome-Based MedicineQuaid Morris, Steven E. Brenner, Jennifer Listgarten, Oliver Stegle; Pacific Symposium on Biocomputing 18:456-458(2013)

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This image was taken by Navcam: Right A (NAV_RIGHT_A) onboard NASA's Mars rover Curiosity on Sol 149 (2013-01-06 05:21:00 UTC) .

Image Credit: NASA/JPL-Caltech

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